Abstract
The rapid spread and severity of pathogens, such as Zika (ZIKV) and Chikungunya (CHIKV) viruses in the Americas, demonstrate the need for a better understanding of when and where outbreaks emerge. Sequence evolution of these viral pathogens occurs simultaneously with geographic spread, which allows phylodynamic processes to be recovered from genomic data. Here, we used time-calibrated phylogeographic analyses implemented in a Bayesian phylogenetic framework to characterize the date of introduction of ZIKV, CHIKV, dengue, and yellow fever viruses in different geographic regions of the Americas. To estimate ‘surveillance gaps’, we compared the estimated dates of introduction of these pathogens to the first confirmations of virus circulation in the region. Datasets included all publicly available geo-referenced and time-stamped genetic data from the Americas. A series of environmental and ecological covariates will be tested to infer what factors are associated with the delayed detection of arbovirus transmission in each geographic region. These results will provide important information on where to concentrate surveillance strengthening measures in order to prevent future mosquito-borne virus epidemics.